Potassium in PDB 6rjr: Crystal Structure of A Fungal Catalase at 1.9 Angstrom
Enzymatic activity of Crystal Structure of A Fungal Catalase at 1.9 Angstrom
All present enzymatic activity of Crystal Structure of A Fungal Catalase at 1.9 Angstrom:
1.11.1.6;
Protein crystallography data
The structure of Crystal Structure of A Fungal Catalase at 1.9 Angstrom, PDB code: 6rjr
was solved by
S.Gomez,
S.Navas-Yuste,
A.M.Payne,
W.Rivera,
M.Lopez-Estepa,
C.Brangbour,
D.Fulla,
J.Juanhuix,
F.J.Fernandez,
M.C.Vega,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.98 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.670,
131.620,
176.670,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.1 /
24.1
|
Other elements in 6rjr:
The structure of Crystal Structure of A Fungal Catalase at 1.9 Angstrom also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom
(pdb code 6rjr). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Crystal Structure of A Fungal Catalase at 1.9 Angstrom, PDB code: 6rjr:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 6rjr
Go back to
Potassium Binding Sites List in 6rjr
Potassium binding site 1 out
of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K609
b:48.2
occ:1.00
|
O
|
A:HOH892
|
2.4
|
24.3
|
1.0
|
O
|
A:GLY208
|
2.5
|
13.7
|
1.0
|
O
|
A:LYS292
|
2.6
|
31.0
|
1.0
|
O
|
A:PRO140
|
2.6
|
14.2
|
1.0
|
O
|
A:HOH819
|
2.8
|
27.1
|
1.0
|
C
|
A:GLY208
|
3.6
|
17.8
|
1.0
|
C
|
A:LYS292
|
3.7
|
24.8
|
1.0
|
C
|
A:PRO140
|
3.8
|
22.4
|
1.0
|
NE2
|
A:GLN224
|
3.8
|
21.4
|
1.0
|
OE1
|
A:GLN224
|
3.9
|
23.9
|
1.0
|
O
|
A:LEU290
|
3.9
|
16.1
|
1.0
|
CA
|
A:GLY208
|
4.1
|
13.4
|
1.0
|
CG1
|
A:VAL141
|
4.2
|
21.6
|
1.0
|
CD
|
A:GLN224
|
4.2
|
21.0
|
1.0
|
CA
|
A:VAL293
|
4.3
|
22.8
|
1.0
|
N
|
A:VAL293
|
4.4
|
13.9
|
1.0
|
C
|
A:LEU290
|
4.5
|
20.7
|
1.0
|
CA
|
A:VAL141
|
4.5
|
22.0
|
1.0
|
N
|
A:LYS292
|
4.6
|
24.3
|
1.0
|
CG1
|
A:VAL293
|
4.6
|
17.1
|
1.0
|
N
|
A:VAL141
|
4.6
|
19.3
|
1.0
|
CA
|
A:PRO140
|
4.7
|
17.4
|
1.0
|
CB
|
A:PRO140
|
4.7
|
27.1
|
1.0
|
O
|
A:ASP289
|
4.8
|
17.5
|
1.0
|
N
|
A:HIS209
|
4.8
|
15.9
|
1.0
|
CA
|
A:LYS292
|
4.8
|
20.6
|
1.0
|
CA
|
A:LEU290
|
4.8
|
19.9
|
1.0
|
O
|
A:HOH926
|
4.9
|
18.9
|
1.0
|
CD1
|
A:LEU290
|
4.9
|
22.8
|
1.0
|
O
|
A:HOH835
|
5.0
|
31.8
|
1.0
|
|
Potassium binding site 2 out
of 4 in 6rjr
Go back to
Potassium Binding Sites List in 6rjr
Potassium binding site 2 out
of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K604
b:72.3
occ:1.00
|
O
|
B:PRO140
|
2.5
|
32.6
|
1.0
|
O
|
B:LYS292
|
2.6
|
45.6
|
1.0
|
O
|
B:HOH804
|
2.6
|
44.8
|
1.0
|
O
|
B:GLY208
|
2.7
|
31.5
|
1.0
|
O
|
B:HOH859
|
2.8
|
36.6
|
1.0
|
C
|
B:LYS292
|
3.7
|
46.8
|
1.0
|
C
|
B:PRO140
|
3.7
|
31.4
|
1.0
|
C
|
B:GLY208
|
3.7
|
44.7
|
1.0
|
O
|
B:LEU290
|
3.8
|
34.5
|
1.0
|
NE2
|
B:GLN224
|
4.1
|
39.0
|
1.0
|
CA
|
B:GLY208
|
4.1
|
31.3
|
1.0
|
CG1
|
B:VAL141
|
4.1
|
32.6
|
1.0
|
OE1
|
B:GLN224
|
4.2
|
44.3
|
1.0
|
CA
|
B:VAL293
|
4.2
|
37.5
|
1.0
|
N
|
B:VAL293
|
4.3
|
46.1
|
1.0
|
CD
|
B:GLN224
|
4.4
|
40.0
|
1.0
|
CA
|
B:VAL141
|
4.5
|
31.5
|
1.0
|
C
|
B:LEU290
|
4.6
|
36.1
|
1.0
|
CA
|
B:PRO140
|
4.6
|
40.9
|
1.0
|
N
|
B:VAL141
|
4.6
|
32.4
|
1.0
|
CB
|
B:PRO140
|
4.6
|
36.8
|
1.0
|
N
|
B:LYS292
|
4.6
|
35.0
|
1.0
|
O
|
B:ASP289
|
4.7
|
29.1
|
1.0
|
CA
|
B:LYS292
|
4.8
|
42.9
|
1.0
|
CB
|
B:VAL293
|
4.8
|
42.5
|
1.0
|
CG2
|
B:VAL293
|
4.9
|
46.6
|
1.0
|
N
|
B:HIS209
|
4.9
|
29.4
|
1.0
|
CA
|
B:LEU290
|
4.9
|
32.4
|
1.0
|
CD1
|
B:LEU290
|
4.9
|
32.6
|
1.0
|
CB
|
B:VAL141
|
5.0
|
31.5
|
1.0
|
|
Potassium binding site 3 out
of 4 in 6rjr
Go back to
Potassium Binding Sites List in 6rjr
Potassium binding site 3 out
of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K605
b:47.0
occ:1.00
|
O
|
C:GLY208
|
2.5
|
16.3
|
1.0
|
O
|
C:LYS292
|
2.6
|
33.6
|
1.0
|
O
|
C:HOH785
|
2.6
|
17.0
|
1.0
|
O
|
C:HOH875
|
2.7
|
27.7
|
1.0
|
O
|
C:PRO140
|
2.7
|
21.1
|
1.0
|
C
|
C:GLY208
|
3.5
|
15.9
|
1.0
|
O
|
C:LEU290
|
3.7
|
28.4
|
1.0
|
NE2
|
C:GLN224
|
3.7
|
27.2
|
1.0
|
C
|
C:LYS292
|
3.8
|
20.5
|
1.0
|
C
|
C:PRO140
|
3.9
|
15.5
|
1.0
|
CA
|
C:GLY208
|
4.1
|
20.3
|
1.0
|
OE1
|
C:GLN224
|
4.2
|
35.3
|
1.0
|
C
|
C:LEU290
|
4.3
|
19.4
|
1.0
|
CG1
|
C:VAL141
|
4.3
|
22.9
|
1.0
|
CD
|
C:GLN224
|
4.3
|
32.4
|
1.0
|
O
|
C:ASP289
|
4.4
|
24.5
|
1.0
|
CA
|
C:VAL293
|
4.5
|
20.0
|
1.0
|
CA
|
C:LEU290
|
4.5
|
17.4
|
1.0
|
CD1
|
C:LEU290
|
4.5
|
19.8
|
1.0
|
N
|
C:VAL293
|
4.6
|
22.2
|
1.0
|
N
|
C:LYS292
|
4.6
|
19.2
|
1.0
|
CA
|
C:VAL141
|
4.6
|
18.8
|
1.0
|
O
|
C:HOH914
|
4.6
|
19.8
|
1.0
|
N
|
C:HIS209
|
4.7
|
26.0
|
1.0
|
O
|
C:HOH878
|
4.7
|
24.0
|
1.0
|
N
|
C:VAL141
|
4.7
|
19.5
|
1.0
|
O
|
C:HOH724
|
4.7
|
44.0
|
1.0
|
CG1
|
C:VAL293
|
4.8
|
16.9
|
1.0
|
CA
|
C:LYS292
|
4.8
|
21.9
|
1.0
|
CA
|
C:PRO140
|
4.9
|
43.9
|
1.0
|
CB
|
C:PRO140
|
5.0
|
27.7
|
1.0
|
CA
|
C:HIS209
|
5.0
|
22.9
|
1.0
|
|
Potassium binding site 4 out
of 4 in 6rjr
Go back to
Potassium Binding Sites List in 6rjr
Potassium binding site 4 out
of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K606
b:53.0
occ:1.00
|
O
|
D:PRO140
|
2.5
|
24.4
|
1.0
|
O
|
D:GLY208
|
2.5
|
19.3
|
1.0
|
O
|
D:LYS292
|
2.6
|
28.7
|
1.0
|
O
|
D:HOH889
|
2.8
|
16.0
|
1.0
|
O
|
D:HOH876
|
2.8
|
41.3
|
1.0
|
C
|
D:GLY208
|
3.5
|
31.9
|
1.0
|
O
|
D:LEU290
|
3.6
|
22.2
|
1.0
|
C
|
D:PRO140
|
3.7
|
18.1
|
1.0
|
C
|
D:LYS292
|
3.8
|
16.6
|
1.0
|
CG1
|
D:VAL141
|
3.8
|
15.4
|
1.0
|
CA
|
D:GLY208
|
3.9
|
12.5
|
1.0
|
NE2
|
D:GLN224
|
4.2
|
30.5
|
1.0
|
C
|
D:LEU290
|
4.2
|
15.2
|
1.0
|
CA
|
D:VAL141
|
4.3
|
16.4
|
1.0
|
OE1
|
D:GLN224
|
4.3
|
24.6
|
1.0
|
CA
|
D:VAL293
|
4.4
|
17.6
|
1.0
|
N
|
D:VAL141
|
4.5
|
20.4
|
1.0
|
N
|
D:VAL293
|
4.5
|
24.4
|
1.0
|
CA
|
D:LEU290
|
4.5
|
20.5
|
1.0
|
N
|
D:LYS292
|
4.5
|
24.2
|
1.0
|
CD1
|
D:LEU290
|
4.6
|
18.8
|
1.0
|
O
|
D:ASP289
|
4.6
|
24.8
|
1.0
|
CD
|
D:GLN224
|
4.6
|
33.3
|
1.0
|
CG1
|
D:VAL293
|
4.6
|
32.3
|
1.0
|
CA
|
D:PRO140
|
4.7
|
24.4
|
1.0
|
N
|
D:HIS209
|
4.7
|
21.4
|
1.0
|
CB
|
D:VAL141
|
4.7
|
28.1
|
1.0
|
CB
|
D:PRO140
|
4.8
|
16.2
|
1.0
|
CA
|
D:LYS292
|
4.8
|
18.6
|
1.0
|
O
|
D:HOH943
|
4.9
|
41.6
|
1.0
|
N
|
D:GLY208
|
5.0
|
27.8
|
1.0
|
|
Reference:
S.Gomez,
S.Navas-Yuste,
A.M.Payne,
W.Rivera,
M.Lopez-Estepa,
C.Brangbour,
D.Fulla,
J.Juanhuix,
F.J.Fernandez,
M.C.Vega.
Peroxisomal Catalases From the Yeasts Pichia Pastoris and Kluyveromyces Lactis As Models For Oxidative Damage in Higher Eukaryotes. Free Radic. Biol. Med. V. 141 279 2019.
ISSN: ISSN 1873-4596
PubMed: 31238127
DOI: 10.1016/J.FREERADBIOMED.2019.06.025
Page generated: Mon Aug 12 17:28:25 2024
|